We prospectively studied 29 consecutive neonates undergoing an arterial switch operation to determine if segmental wall motion abnormalities (SWMA) represented myocardial ischemia. Intraoperative transesophageal echocardiogram was recorded at baseline and twice after cardiopulmonary bypass. Cardiac troponin I (cTnI) levels were measured before sternal incision and 3, 6, 12, 24, 48, and 72 h after removal of the aortic cross-clamp. Immediate postoperative Holter and 15-lead electrocardiograms (ECG) were evaluated for ischemia. Transthoracic echocardiograms were obtained before hospital discharge. At bypass termination, immediately after protamine administration, segmental wall motion was normal in nine neonates and abnormal in 20. SWMA were transient in five and present at the time of chest closure in 15 neonates. Neonates in whom SWMA were present at chest closure had more segments involved than those in whom SWMA were transient (P > 0.001). Neonates with SWMA at chest closure had higher cTnI levels postoperatively versus neonates with normal wall motion (P = 0.02). Postoperative ECG data were available in 26 neonates. There was ECG evidence of myocardial ischemia in two of eight neonates with normal wall motion, one of five with transient SWMA, and nine of 13 with SWMA at chest closure. CTnI levels at 12, 24, and 48 h and intraoperative SWMA were predictive of postoperative SWMA. We believe these data indicate that SWMA, which persist at the completion of an arterial switch operation, and which are present in multiple myocardial segments, correlate with myocardial ischemia. Further follow-up of these patients is needed to determine if increased intraoperative myocardial ischemia correlates with long-term outcomes.